Table 2. Five gene clusters showing transcriptional upregulation in TKI-resistant K562 sublines.

Upregulation	Cluster	Gene symbols
Nilotinib	1	TMEM51, PLA2G4A, KIF1A, C2orf14, OSBPL6, LOC152078, ENTPD3, ENC1, MAP7, LAMB1, CD36, ABCB1, C9orf125, CASP4, HMGA2, NTS, TRHDE, LOC144766, TEX9, ZNF447, AURKC, FAM9B, NXF5, NXF2, SSX3
	4	IL1R1, COLEC11, ZNF354A, C6orf85, SPTAN1, KCNMB4, ARHGDIB, MGC16044, FAM9A, VCY, VCY1B
	8	ARHGAP15, COBLL1, ANTXR1, ITGA4, FMNL2, TNFSF10, FLJ31033, APIN, ZDHHC11, SLCO4C1, CD109, ZNF462, CHST3, MRPS16, MS4A4A, PAK1, DACH1, DCT, STRA6, BC036928, ASB9
Nilotinib and Imatinib	2	SERINC2, KYNU, GAD1, ANKRD20B, CTDSPL, FLJ20647, SNCA, PPP3CA, ELOVL7, PANK3, SLC12A7, TAP1, HEY1, RGS20, ZFHX4, LOC441395, C10orf38, AKR1CL2, C10orf71, CD44, IFITM3, PTPRR, SPRY2, MGAT2, PRKCH, C14orf39, COTL1, PMP22, ZNF420, ZNF85, ZNF567, LILRB1, ZNF626, SYTL4, SSX6, TCEAL4
	9	AIM2, PTPRC, FAM5C, TNFRSF9, NR5A2, CD1D, CDC42EP3, MEIS1, IFIH1, GCA, PTX3, BOMB, EGF, DAB2, LOC493869, LAMA4, TPBG, SYK, TLE4, SFXN3, MCAM, ADM, MLSTD1, LRMP, NIN, CHES1, ABCA8, ZNF527, HKR1, JAG1, CPXM, SLC35E4, COVA1

Abbreviation: TKI, tyrosine kinase inhibitors.

The five gene clusters are selected among 12 K-means clusters and illustrated with genes. Three clusters (Cluster 1, 4 and 8; upper) contain genes upregulated in nilotinib-resistant cell lines and two other clusters (Cluster 2 and 9; below) contain genes showing upregulation in both nilotinib- and imatinib-resistant cell lines.